Quick users guide

Setting up to image:

1.  Boot the IMAGING computer; open LabView.

2.  Open the LabView project, currently called "tsetprojwholething.lvproj"

3.  Plug in the camera

4.  Wait until you are ready to image; use the MASTER computer to start the "Brain Surface Imaging" panel; the settings for coarse direction are as follows:  Reps 20-40, ISI 15, angles [0:45:135], change edit base as usual; 'Run' the stimulus; hold up at the point where the analysis computer says 'Confirm acquisition is running'

5.  Back on the IMAGING computer, go into the project and right-click on the file 'ccd_imaging' to bring up a menu, and choose 'Run'

5.  Click "Live imaging" to focus. Use green light (by adjusting the LED brightness using the manual knob) to take a picture of the surface vessels.  Then adjust the red light (again using the manual knob) so the brain is just below saturation (use the histograms and the cursor to examine brightness values at different portions of the image).

6.  Close the window and click the Stop sign to stop the program from running.

7.  Go to the LabView project window again and right-click on the file 'ccd_triggeredacquisition' to bring up a menu, and choose 'Run'.

8.  Click the "GO" button to begin waiting for triggers.  Verify that the correct directory appears in the dirname field.

9.  On the MASTER computer, give the final okay to run the stimulus


Analysis:

 you can change the frames to be analyzed between [3 5] to [3 10]; and the median filter can be set to 50, 100, 200 or 300. 

Right now there is a bit of analysis code that is missing.  One needs to tell the software which conditions were run and the order that the stimuli were displayed in.  To do this, run the following lines 

cd DIRECTORY  (DIRECTORY might be C:\remote\2011-03-30\t00002)
stimvalues = [0:45:360-45 NaN];
save('stimvalues','stimvalues');
g = load('stims.mat');
stimorder = getDisplayOrder(g.saveScript);
save('stimorder','stimorder');


CHANGE IN REFLECTANCE / REFLECTANCE

(Rstim - Rbefore)/Rbefore

Rbefore = the average of data frames 1 and 2
Rstim = the average of data frames 3:10



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